mperr1 at hamon.swmed.edu (Michael Perry) wrote:
>Chris,
>Sounds like a job for blastx. Point your browser to the NCBI BLAST
>web page at http://www.ncbi.nlm.nih.gov/BLAST/ and check out the
>following programs:
>blastx: compares a nucleotide query sequence translated in all
>reading frames against a protein sequence database
>tblastx: compares the six-frame translations of a nucleotide query
>sequence against the six-frame translations of a nucleotide sequence
>database.
Thanks for the reply but I tried that first. What it appears to do is
compare the entire sequence (as if it were a single ORF) in all 6
frames. What I would like to do is have it blast the real ORFs >30
amino acids individually. When I blast them manually, it brings back
different hits than a blastx search of the entire sequence.
As an example, when I blast one of the 200 aa ORFs it returns an EST
clone. When I blast the entire sequence, of which this ORF is just a
part, it doesnt show up. Hopefully I explained that clearly!
Any other ideas would be appreciated!
********************************************************************
Chris Kafer Lab: 2228 Mol. Bio. Bldg. Ph#: 515-294-8626
http://www.public.iastate.edu/~ippmhttp://www.public.iastate.edu/~thorn
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"...it is those who know little, and not those who know much, who so
positively assert that this or that problem will never be solved by
science." Charles Darwin, from The Descent of Man